Characterization of Arsenic-Resistant Klebsiella pneumoniae RnASA11 from Contaminated Soil and Water Samples and Its Bioremediation Potential

Cu-tolerant Klebsiella variicola SRB-4 increased the nanoparticle (NP) stress resilience in garden peas (Pisum sativum L.) raised in soil polluted with varying doses of copper oxide (CuO)-NP

Utilizing metal/nanoparticle (NP)- tolerant plant growth-promoting rhizobacteria (PGPR) is a sustainable and eco-friendly approach for remediation of NP-induced phytotoxicity. Here, Pisum sativum (L.) plants co-cultivated with different CuO-NP concentrations exhibited reduced growth, leaf pigments, yield attributes, and increased oxidative stress levels. Cu-tolerant (800 µM) Klebsiella variicola strain SRB-4 (Accession no. OR715781.1) recovered from metal-contaminated soils produced various PGP traits, including IAA, EPS, siderophore, HCN, ammonia, and solubilized insoluble P. The PGP substances were marginally increased with increasing CuO-NP concentrations. When applied, Cu-tolerant SRB-4 strain increased root length (18%), root biomass (15.3%), total chlorophyll (29%), carotenoids (30%), root N (21%), root P (23%), total soluble protein (20%) nodule number (32%), nodule biomass (39%) and leghaemoglobin content (18%) in 50 µM CuO-NP-exposed peas. Furthermore, proline, malondialdehyde (MDA), superoxide radical, hydrogen peroxide (H2O2) content, and membrane injury in K. variicola-inoculated and 50 µM CuO-NP-treated plants were maximally and significantly (p ≤ 0.05) reduced by 70.6, 26.8, 60.8, and 71.6%, respectively, over uninoculated but treated with similar NP doses. Moreover, K. variicola inoculation caused a significant (p ≤ 0.05) decline in Cu uptake in roots (71%), shoots (65.5%), and grains (76.4%) of peas grown in soil contaminated with 50 µM CuO-NP. The multivariate i.e. heat map and pearson correlation analyses between the NP-treated and PGPR inoculated parameters revealed a significant and strong positive corelation. The NP-tolerant indigenous beneficial K. variicola could be applied as an alternative to enhance the production of P. sativum cultivated in nano-polluted soil systems. Additionally, more investigation is required to ascertain the seed/soil inoculation effect of K. variicola SRB-4 on soil biological activities and different crops under various experimental setups.

Unravelling the mechanism of arsenic resistance and bioremediation in Stenotrophomonas maltophilia: A molecular approach

The mechanism of arsenic resistance in bacteria is under studied and still lacks a clear understanding despite of wide research work. The advanced technologies can help in analysing the arsenic bioremediating bacteria at a molecular level. With this line of idea, highly efficient arsenic bioremediating S. maltophilia was subjected to extensive analysis to understand the mechanism of arsenic resistance and bioremediation. The cell surface analysis revealed that S. maltophilia induces only slight changes in cell surface in the presence of arsenic. Whereas, TEM analysis has indicated the bioaccumulation of arsenic in S. maltophilia. Also, arsenic was found to generate ROS in a concentration dependant manner, and in response, S. maltophilia activated SOD, catalase, thioredoxin reductase etc. to manage oxidative stress which is very much crucial in managing arsenic toxicity. S. maltophilia was found to possess genes such as arsC, aoxB, aoxC and aioA. These genes are involved in arsenic reduction and oxidation. Transcriptomics and proteomics analysis have shown that S. maltophilia detoxifies arsenic by upregulating ars operon, arsH, BetB etc. which are responsible for arsenic reduction, efflux methylation, oxidation etc. A detailed molecular mechanism of arsenic bioremediation in S. maltophilia was put forth.

Alleviating arsenic stress affecting the growth of Vigna radiata through the application of Klebsiella strain ASBT-KP1 isolated from wastewater

Arsenic contamination of soil and water is a major environmental issue. Bioremediation through plant growth-promoting bacteria is viable, cost-effective, and sustainable. Along with arsenic removal, it also improves plant productivity under stressful conditions. A crucial aspect of such a strategy is the selection of bacterial inoculum. The described study demonstrates that the indigenous wastewater isolate, ASBT-KP1, could be a promising candidate. Identified as Klebsiella pneumoniae, ASBT-KP1 harbors genes associated with heavy metal and oxidative stress resistance, production of antimicrobial compounds and growth-promotion activity. The isolate efficiently accumulated 30 μg/g bacterial dry mass of arsenic. Tolerance toward arsenate and arsenite was 120 mM and 70 mM, respectively. Plant biomass content of Vigna radiata improved by 13% when grown in arsenic-free soil under laboratory conditions in the presence of the isolate. The increase became even more significant under the same conditions in the presence of arsenic, recording a 37% increase. The phylogenetic analysis assigned ASBT-KP1 to the clade of Klebsiella strains that promote plant growth. Similar results were also observed in Oryza sativa, employed to assess the ability of the strain to promote growth, in plants other than V. radiata. This study identifies a prospective candidate in ASBT-KP1 that could be employed as a plant growth-promoting rhizoinoculant in agricultural practices.

Identification of arsenic oxidizing genes fragment in Microbacterium sp. strain 1S1 and its cloning in E. coli (DH5a)

Microbacterium sp. strain 1S1, an arsenic-resistant bacterial strain, was isolated with 75 mM MIC against arsenite. Brownish precipitation with silver nitrate appeared, which confirmed its oxidizing ability against arsenite. The bacterial genomic DNA underwent Illumina and Nanopore sequencing, revealing a distinctive cluster of genes spanning 9.6 kb associated with arsenite oxidation. These genes were identified within an isolated bacterial strain. Notably, the smaller subunit (aioB) of the arsenite oxidizing gene at the chromosomal DNA locus (Prokka_01508) was pinpointed. This gene, aioB, is pivotal in arsenite oxidation, a process crucial for energy metabolism. Upon thorough sequencing analysis, only a singular megaplasmid was detected within the isolated bacterial strain. Strikingly, this megaplasmid did not harbor any genes responsible for arsenic resistance or detoxification. This intriguingly indicates that the bacterial strain relies on the arsenic oxidizing genes present for its efficient arsenic oxidation capability. This is especially true for Microbacterium sp. strain 1S1. Subsequently, a segment of genes linked to arsenic resistance was successfully cloned into E. coli (DH5a). The fragment of arsenic-resistant genes was cloned in E. coli (DH5a), further confirmed by the AgNO3 method. This genetically engineered E. coli (DH5a) can decontaminate arsenic-contaminated sites.

Heavy-metal tolerant bacterial strains isolated from industrial sites and scrap yards in Kashmir, India

Heavy metal pollution has posed a severe danger to environmental stability due to its high toxicity and lack of biodegradability. The present study deals with the appraisement of tolerance shown by various bacteria in varied copper and iron concentrations. Among the 20 isolates, four isolates, GN2, SC5, SC8, and SC10, exhibiting more significant iron and copper tolerance, were selected and identified by 16 S ribosomal ribonucleic acid (rRNA) gene sequence analysis as Pantoea agglomerans strain GN2, Pantoea sp. strain SC5, Bacillus sp. strain SC8 and Priestia aryabhattaistrain SC10. The minimum inhibitory concentration of molecularly identified strains revealed that P. agglomerans strain GN2 showed tolerance to iron sulfate and copper sulfate upto 600 and 400 µg/mL, whereas Bacillus sp. SC8 (OQ202165) showed tolerance of 700 and 250 µg/mL were tolerant to iron sulfate and copper sulfate up to 700 and 150 µg/mL, respectively. Pantoea sp. strain SC5 showed significant tolerance to both heavy metals. The isolates were further studied for their ability to grow at varying temperatures and pH ranges. Most of the isolates showed optimal growth at 37°C and pH 7. However, Pantoea sp. SC5 was competent to have prominent growth at 45°C and pH 8.0. Microbial remediation, which is eco-friendly, has proven the most effective method for bioremediation of heavy metal-contaminated environments. Using heavy metal-resistant bacteria for microbial remediation of iron and copper-contaminated environments could be a viable and valuable strategy. These isolates could also be used to decontaminate heavy metal-polluted agricultural soils.

Isolation and Identification of Arsenic-Resistant Extremophilic Bacteria from the Crater-Lake Volcano "El Chichon", Mexico

The crater lake at "El Chichón" volcano is an extreme acid-thermal environment with high concentrations of heavy metals. In this study, two bacterial strains with the ability to resist high concentrations of arsenic (As) were isolated from water samples from the crater lake. Staphylococcus ARSC1-P and Stenotrophomonas ARSC2-V isolates were identified by use of the 16S rDNA gene. Staphylococcus ARSC1-P was able to grow in 400 mM of arsenate [As(V)] under oxic and anoxic conditions. The IC₅₀ values were 36 and 382 mM for oxic and anoxic conditions, respectively. For its part, Stenotrophomonas ARSC2-V showed IC₅₀ values of 110 mM and 2.15 for As(V) and arsenite [As(III)], respectively. Arsenic accumulated intracellularly in both species [11-25 nmol As × mg cellular prot^-1 in cells cultured in 50 mM As(V)]. The present study shows evidence of microbes that can potentially be a resource for the bio-treatment of arsenic in contaminated sites, which highlights the importance of the "El Chichón" volcano as a source of bacterial strains that are adaptable to extreme conditions.

Arsenic and mercury tolerant rhizobacteria that can improve phytoremediation of heavy metal contaminated soils

Background

Mining deposits often contain high levels of toxic elements such as mercury (Hg) and arsenic (As) representing strong environmental hazards. The purpose of this study was the isolation for plant growth promoting bacteria (PGPBs) that can improve phytoremediation of such mine waste deposits.

Methods

We isolated native soil bacteria from the rhizosphere of plants of mine waste deposits and agricultural land that was previously mine tailings from Tlalpujahua Michoacán, Mexico, and were identified by their fatty acid profile according to the MIDI Sherlock system. Plant growth promoting traits of all bacterial isolates were examined including production of 3-indoleacetic acid (IAA), siderophores, biofilm formation, and phosphate solubilization. Finally, the response of selected bacteria to mercury and arsenic was examined an in-vitro assay.

Results

A total 99 bacterial strains were isolated and 48 identified, representing 34 species belonging to 23 genera. Sixty six percent of the isolates produced IAA of which Pseudomonas fluorescens TL97 produced the most. Herbaspirillum huttiense TL36 performed best in terms of phosphate solubilization and production of siderophores. In terms of biofilm formation, Bacillus atrophaeus TL76 was the best.

Discussion

Most of the bacteria isolates showed high level of tolerance to the arsenic (as HAsNa₂O₄ and AsNaO₂), whereas most isolates were susceptible to HgCl₂. Three of the selected bacteria with PGP traits Herbispirillum huttiense TL36, Klebsiella oxytoca TL49 and Rhizobium radiobacter TL52 were also tolerant to high concentrations of mercury chloride, this might could be used for restoring or phytoremediating the adverse environmental conditions present in mine waste deposits.

Effects of chronic exposure to arsenic on the fecal carriage of antibiotic-resistant Escherichia coli among people in rural Bangladesh

Antibiotic resistance is a leading cause of hospitalization and death worldwide. Heavy metals such as arsenic have been shown to drive co-selection of antibiotic resistance, suggesting arsenic-contaminated drinking water is a risk factor for antibiotic resistance carriage. This study aimed to determine the prevalence and abundance of antibiotic-resistant Escherichia coli (AR-Ec) among people and drinking water in high (Hajiganj, >100 μg/L) and low arsenic-contaminated (Matlab, <20 μg/L) areas in Bangladesh. Drinking water and stool from mothers and their children (<1 year) were collected from 50 households per area. AR-Ec was detected via selective culture plating and isolates were tested for antibiotic resistance, arsenic resistance, and diarrheagenic genes by PCR. Whole-genome sequencing (WGS) analysis was done for 30 E. coli isolates from 10 households. Prevalence of AR-Ec was significantly higher in water in Hajiganj (48%) compared to water in Matlab (22%, p <0.05) and among children in Hajiganj (94%) compared to children in Matlab (76%, p <0.05), but not among mothers. A significantly higher proportion of E. coli isolates from Hajiganj were multidrug-resistant (83%) compared to isolates from Matlab (71%, p <0.05). Co-resistance to arsenic and multiple antibiotics (MAR index >0.2) was observed in a higher proportion of water (78%) and child stool (100%) isolates in Hajiganj than in water (57%) and children (89%) in Matlab (p <0.05). The odds of arsenic-resistant bacteria being resistant to third-generation cephalosporin antibiotics were higher compared to arsenic-sensitive bacteria (odds ratios, OR 1.2-7.0, p <0.01). WGS-based phylogenetic analysis of E. coli isolates did not reveal any clustering based on arsenic exposure and no significant difference in resistome was found among the isolates between the two areas. The positive association detected between arsenic exposure and antibiotic resistance carriage among children in arsenic-affected areas in Bangladesh is an important public health concern that warrants redoubling efforts to reduce arsenic exposure.

Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria

Marker proteins play a significant role in bacterial arsenic (As) transformation. Phylogenetic analysis and three-dimensional (3D) characteristics of As transforming bacterial marker proteins guide the evolutionary origin and As transforming potential of the species. Indeed, As-tolerant bacteria also show a significant level of As transformation. Hence, characterization of As transforming bacterial marker proteins, isolation of As transforming bacteria, and proper integration of the findings may guide to elucidate how bacteria transform As. Therefore, phylogenetic analysis and 3D characterization of As transforming bacterial marker protein following isolation of potential indigenous As-tolerant indigenous bacteria were done to explore the mechanism of bacterial As transformation. Phylogenetic analysis of ten As transforming marker proteins (arsA, arsB, arsC, arsD, arsR, aioA, arrA, aioB, acr1, and acr3) in 20 potential bacterial genomes (except 19 for the acr3) were studied. Some bacterial genomes featured up to five marker proteins, and therefore, 3D characteristics of the marker proteins were analyzed in those genomes having three-to-five marker proteins. In phylogeny, species in close clades represent their phylogenetic resemblances and may have similar functions. P. aeruginosa, E. coli, and K. pneumonia were found to be more effective due to having the highest number (five) of marker proteins. In 3D protein modeling, most of the marker proteins were found to be active. Among 19 indigenous bacterial isolates, multiple isolates showed tolerance up to 50 mM As(III) and 250 mM As(V), which may potentially transform a significant quantities of As. Hence, integration of the results of phylogenetic analysis, 3D protein characteristics, and As tolerance in the bacterial isolates could guide to explore the mechanism of how bacteria transform As at cellular and molecular levels.